7NTG
Bdellovibrio bacteriovorus PGI in complex with fructose-6-phosphate
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7NSS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5 | 291 | 0.2 M ammonium acetate 0.1 M sodium acetate pH 5.0 20% PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.2 | α = 90 |
b = 101.2 | β = 90 |
c = 76.38 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2019-08-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97951 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
1 | 1.67 | 43.82 | 99.9 | 0.057 | 0.06 | 0.019 | 1 | 25 | 19.6 | 52651 | 41.07 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.67 | 1.7 | 99.9 | 1.966 | 2.073 | 0.655 | 0.822 | 1.5 | 19.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 7NSS | 1.67 | 43.82 | 50006 | 2616 | 97.02 | 0.1799 | 0.1781 | 0.2167 | RANDOM | 36.123 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.85 | 0.43 | 0.85 | -2.77 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.564 |
r_dihedral_angle_4_deg | 19.793 |
r_dihedral_angle_3_deg | 13.734 |
r_dihedral_angle_1_deg | 6.62 |
r_angle_other_deg | 2.293 |
r_angle_refined_deg | 1.63 |
r_chiral_restr | 0.089 |
r_bond_other_d | 0.034 |
r_gen_planes_other | 0.013 |
r_bond_refined_d | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3163 |
Nucleic Acid Atoms | |
Solvent Atoms | 283 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |
xia2 | data reduction |